Optimization of scientific algorithms in heterogeneous systems and accelerators for high performance computing

Actualmente, la computación de propósito general en GPU es uno de los pilares básicos de la computación de alto rendimiento. Aunque existen cientos de aplicaciones aceleradas en GPU, aún hay algoritmos científicos poco estudiados. Por ello, la motivación de esta tesis ha sido investigar la posibilidad de acelerar significativamente en GPU un conjunto de algoritmos pertenecientes a este grupo. En primer lugar, se ha obtenido una implementación optimizada del algoritmo de compresión de vídeo e imagen CAVLC (Context-Adaptive Variable Length Encoding), que es el método entrópico más usado en el estándar de codificación de vídeo H.264. La aceleración respecto a la mejor implementación anterior está entre 2.5x y 5.4x. Esta solución puede aprovecharse como el componente entrópico de codificadores H.264 software, y utilizarse en sistemas de compresión de vídeo e imagen en formatos distintos a H.264, como imágenes médicas. En segundo lugar, se ha desarrollado GUD-Canny, un detector de bordes de Canny no supervisado y distribuido. El sistema resuelve las principales limitaciones de las implementaciones del algoritmo de Canny, que son el cuello de botella causado por el proceso de histéresis y el uso de umbrales de histéresis fijos. Dada una imagen, esta se divide en un conjunto de sub-imágenes, y, para cada una de ellas, se calcula de forma no supervisada un par de umbrales de histéresis utilizando el método de MedinaCarnicer. El detector satisface el requisito de tiempo real, al ser 0.35 ms el tiempo promedio en detectar los bordes de una imagen 512x512. En tercer lugar, se ha realizado una implementación optimizada del método de compresión de datos VLE (Variable-Length Encoding), que es 2.6x más rápida en promedio que la mejor implementación anterior. Además, esta solución incluye un nuevo método scan inter-bloque, que se puede usar para acelerar la propia operación scan y otros algoritmos, como el de compactación. En el caso de la operación scan, se logra una aceleración de 1.62x si se usa el método propuesto en lugar del utilizado en la mejor implementación anterior de VLE. Esta tesis doctoral concluye con un capítulo sobre futuros trabajos de investigación que se pueden plantear a partir de sus contribuciones

CUVLE: Variable-Length Encoding on CUDA

Data compression is the process of representing information in a compact form, in order to reduce the storage requirements and, hence, communication bandwidth. It has been one of the critical enabling technologies for the ongoing digital multimedia revolution for decades. In the variable-length encoding (VLE) compression method, most frequently occurring symbols are replaced by codes with shorter lengths. As it is a common strategy in many compression applications, efficient parallel implementations of VLE are very desirable. In this paper we present CUVLE, a GPU implementation of VLE on CUDA. Our approach is on average more than 20 and 2 times faster than the corresponding CPU serial implementation and the only known state-of-the-art GPU implementation, respectively.Junta de Andalucía, TIC-1692. Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

CAVLCU: an efficient GPU-based implementation of CAVLC

CAVLC (Context-Adaptive Variable Length Coding) is a high-performance entropy method for video and image compression. It is the most commonly used entropy method in the video standard H.264. In recent years, several hardware accelerators for CAVLC have been designed. In contrast, high-performance software implementations of CAVLC (e.g., GPU-based) are scarce. A high-performance GPU-based implementation of CAVLC is desirable in several scenarios. On the one hand, it can be exploited as the entropy component in GPU-based H.264 encoders, which are a very suitable solution when GPU built-in H.264 hardware encoders lack certain necessary functionality, such as data encryption and information hiding. On the other hand, a GPU-based implementation of CAVLC can be reused in a wide variety of GPU-based compression systems for encoding images and videos in formats other than H.264, such as medical images. This is not possible with hardware implementations of CAVLC, as they are non-separable components of hardware H.264 encoders. In this paper, we present CAVLCU, an efficient implementation of CAVLC on GPU, which is based on four key ideas. First, we use only one kernel to avoid the long latency global memory accesses required to transmit intermediate results among different kernels, and the costly launches and terminations of additional kernels. Second, we apply an efficient synchronization mechanism for thread-blocks (In this paper, to prevent confusion, a block of pixels of a frame will be referred to as simply block and a GPU thread block as thread-block.) that process adjacent frame regions (in horizontal and vertical dimensions) to share results in global memory space. Third, we exploit fully the available global memory bandwidth by using vectorized loads to move directly the quantized transform coefficients to registers. Fourth, we use register tiling to implement the zigzag sorting, thus obtaining high instruction-level parallelism. An exhaustive experimental evaluation showed that our approach is between 2.5x and 5.4x faster than the only state-of-the-art GPUbased implementation of CAVLC.ISSN:0920-8542ISSN:1573-048

Modelling the growth boundaries of Staphylococcus aureus: Effect of temperature, pH and water activity

The microbial behaviour of five enterotoxigenic strains of Staphylococcus aureus was studied in the growth/no growth domain. A polynomial logistic regression equation was fitted using a stepwise method to study the interaction of temperature (8, 10, 13, 16 and 19 °C), pH (4.5; 5.0; 5.5; 6.0; 6.5 7.0 and 7.5) and water activity (Aw) (19 levels ranging from 0.867 to 0.999) on the probability of growth. Out of the 284 conditions tested, 146 were chosen for model data and 138 intermediate conditions for validation data. A growth/no growth transition was obtained by increasing the number of replicates per condition (n = 30) in comparison to other published studies. The logistic regression model showed a good performance since 96.6% (141 out of 146 conditions) of the conditions for model data and 92.0% (127 out of 138 conditions) for validation data were correctly classified. The predictions indicated an abrupt growth/no growth interfaces occurred at low levels of temperature, pH and Aw. At 8 °C, S. aureus grew only at optimum levels of pH and Aw while at temperatures above 13 °C, growth of S. aureus was observed at pH = 4.5 and Aw = 0.96 (13 °C), 0.941 (16 °C) and 0.915 (19 °C). The optimal pH at which growth of S. aureus was detected earlier was 6.5. However, a slight decrease of the probability of growth was noticed in the pH interval of 7.0–7.5 at more stringent conditions. The ability of S. aureus to grow at low Aw was shown since growth was detected at Aw = 0.867 (T = 19 °C; pH = 7.0). Finally, a comparison of model predictions with literature data on growth/no growth responses of S. aureus in culture media and cooked meat was made. Model predictions agreed with published data in 94% of growth cases and in 62% of no growth cases. The latter discordance is highly associated to other environmental factors (such as other preservatives, strains etc.) included in published models that did not match the ones included in our study. This study can help manufacturers in making decision on the most appropriate formulations for food products in order to prevent S. aureus growth and enterotoxin production along their shelf-life.This work was partly financed by MICINN AGL2008-03298/ALI, the Excellence Project AGR-01879 (Junta de Andalucía) and by European ERDF funding.Peer reviewe

Micro-scale distribution of recently-detached Carybdea marsupialis box jellyfish along the coast of Denia (W. Mediterranean)

5th International Jellyfish Bloom Symposium, 30 May to 3 June 2016, Barcelona.-- 1 pageCarybdea marsupialis have been found in high densities (~90 ind m3 juveniles, ~51 ind m3 adults) in shallow waters along the coast of Denia (W. Mediterranean) since summer 2008, varying significantly in abundance from year to year. In order study the role of juvenile stages in population dynamics, we analyzed the seasonal and micro-scale spatial distribution of recently-detached cubomedusae (~0.5 mm DBW). The main objective was to determine whether their distribution was focused or dispersed, as a means of revealing the location of the polyps. We also tested the correlation between environmental variables such as nutrient (P, N, Si), Chl-a and zooplankton abundance. During 2015 we collected samples from 33 points: 11 points along 15km of coastline at 3 distances from the coast (0m, 250m and 500m). Recently-detached C. marsupialis were almost only present at a depth of 0m in the samples collected from May to July. Maximum densities (~5 ind m3) were recorded in June in the centre of the study area. We hypothesized that the polyps would be located where the adults had mated the previous year. However, the distribution of recently-detached individuals did not coincide with the higher 2014 adult densities. This might be ascribed to the advection caused by the currents, which alternate along the coast. Abundance was not directly correlated with either zooplankton, nutrients or Chl-a. The next step would be to model the currents pattern and its effect in the dispersion and survival of juvenilesPeer Reviewe

3,4-Dihydroxyphenylglycol (DHPG): An Important Phenolic Compound Present in Natural Table Olives

The presence of 3,4-dihydroxyphenylglycol (DHPG) was studied in 32 samples and 10 different cultivars of natural table olives, using an accurate method to avoid wrong quantification. Hydroxytyrosol (HT), tyrosol, and verbascoside were also quantified, as these four compounds comprise the majority of the chromatographic profile. Analyses were carried out by HPLC-DAD-UV after extraction of all phenolics, and hydroxytyrosol was the major component in nearly all samples. High levels of DHPG (up to 368 mg/kg of dry weight) were found in the pulp of natural black olives independent of cultivar and processing method, similar to its concentration in the brine in almost all of the samples. The presented data for this antioxidant indicate that natural table olives are a rich source of DHPG and hydroxytyrosol, compounds with interesting nutritional and antioxidant properties.This work was supported by the Ministerio de Educación y Ciencia through Grants AGL2005-00616-ALi/AGL2008-02590-ALI and AGL2007-66373-CO4-01-ALI. We thank the Junta de Andalucía (PO6-AGR-01906) for financial support.Peer reviewe

Effect of extraction method on chemical composition and functional characteristics of high dietary fibre powders obtained from asparagus by-products

Asparagus (Asparagus officinalis L.) by-products, which represent around 50% of the processed vegetable, are a potential source of dietary fibre. The way that these by-products are treated affects the composition and functional properties of fibre-rich powders. Factors such as treatment intensity, solvent, and drying system were studied. Only the more soluble components (soluble sugars, uronic acids and proteins) showed significant differences. All the fibre-rich powders had high concentrations of TDF (62–77%). The IF/SF proportion decreased with the severity of treatment, in this way increasing the physiological quality of the fibre. Functional properties, namely water-holding capacity (WHC), oil-holding capacity (OHC), solubility (SOL), and glucose dialysis retardation index (GDRI), varied according to the preparation procedure. WHC and GDRI were higher in intensely extracted fibres; due to the effect of thermal processing. WHC showed values (11–20 ml water/g powder) similar to those described for other agricultural by-products, but OHC and GDRI were much higher (5–8 ml oil/g powder and 25–45%, respectively). These properties make fibre-rich powders from asparagus by-products a valuable source of dietary fibre to be included in the formulation of fibre-enriched foods.This research was supported by the Ministerio de Ciencia y Tecnología (Spain), Proyect PETRI PTR1995-0968-OP.Peer reviewe

Pectin extracted from thermally treated olive oil by-products: Characterization, physico-chemical properties, invitro bile acid andglucose binding

© 2014 Elsevier Ltd. The pectin fraction released from steam-treated alperujo at 160°C for 30, 45, and 60min was purified and characterized. Differences were observed in the composition, and physical and biological activities of the pectin extracts, depending on the length of the thermal treatment. The extracts presented a low molecular weight in the range of 2-40KDa, a high content of neutral sugars, and a high percentage of acetylation. In comparison with commercial pectins, the extracts had low water and high oil holding capacities, a normal emulsifying activity and a similar emulsion stability to that of apple pectin. For the three pectin extracts studied, the invitro analyses showed considerable bile-acid binding activity and a glucose retardation index similar to the values obtained for citrus pectins. Thus, the pectins isolated from olive oil waste have suitable physical and biological properties for commercial use. Pectin extraction from alperujo, a sizeable by-product of the olive oil manufacturing process, would facilitate the use and subsequent reduction of this environmentally damaging organic waste.Funding was received from the Ministerio de Economía y Competitividad of Spain and co-funded by European Social Fund (ESF) (project AGL2013-48291-R). F.R.S. received funding from the Spanish JAE-PRE program (CSIC-ESF).Peer Reviewe